[SYNPY-1544] Synapse Agent OOP Model #1152

BWMac · 2025-01-08T19:49:48Z

WIP

Implementation of design doc: https://sagebionetworks.jira.com/wiki/spaces/DPE/pages/3833954306/SYNPY-1544+Synapse+Agent+OOP+Model+Mini-Design

pep8speaks · 2025-01-08T19:50:00Z

Hello @BWMac! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

In the file synapseclient/api/agent_services.py:

Line 80:89: E501 line too long (89 > 88 characters)
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In the file synapseclient/models/agent.py:

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In the file synapseclient/models/mixins/asynchronous_job.py:

Line 94:89: E501 line too long (125 > 88 characters)
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In the file synapseclient/models/protocols/agent_protocol.py:

Line 20:89: E501 line too long (112 > 88 characters)
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In the file tests/unit/synapseclient/mixins/async/unit_test_asynchronous_job.py:

Line 65:15: E999 SyntaxError: invalid syntax
Line 128:89: E501 line too long (104 > 88 characters)
Line 141:89: E501 line too long (92 > 88 characters)
Line 146:89: E501 line too long (92 > 88 characters)

Comment last updated at 2025-01-16 14:57:29 UTC

synapseclient/api/agent_services.py

BryanFauble · 2025-01-08T22:32:12Z

synapseclient/api/agent_services.py

+    start_time = asyncio.get_event_loop().time()
+    TIMEOUT = 60
+
+    while True:


synapsePythonClient/synapseclient/client.py

Line 5029 in 8bd5e19

def _waitForAsync(self, uri, request, endpoint=None):

This function exists on the client, but it not built with asyncio in mind. There is some additional error handling it does for the failed state. I could see an asyncio compliant version being written and used here.

Maybe it could go in this file? https://github.com/Sage-Bionetworks/synapsePythonClient/blob/8bd5e195c389e3a83bd1308be3c6a42f25d87b8f/synapseclient/core/async_utils.py

_waitForAync does both the POST call (starting the job) and the GET call (retrieving the result). Should the functionality I have written here work that way too? I was viewing it as 1 function per API endpoint in agent_services originally.

I can still write a reusable async function for getting the response and handling incomplete and failed jobs, but just wondering what you think about division of responsibility there.

They can be 2 separate functions that handle each part. In the Agent script you'll chain them together

synapseclient/api/agent_services.py

synapseclient/models/agent.py

BryanFauble · 2025-01-08T22:46:00Z

synapseclient/models/agent.py

+    """
+    Enum representing the type of agent as defined in
+        <https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/agent/AgentType.html>
+    'BASELINE' is a default agent provided by Synapse.


Nit. Can be a list. Syntax is a empty newline before and each entry starts with -.

Might need to make sure it renders properly on my docs.

Related to ^
These will be "Less" experimental APIs, so we can add a new non-experimental section to

synapsePythonClient/mkdocs.yml

Line 55 in 8bd5e19

- API Reference:

for this. Not sure on the title, maybe "AI Agent" or something?

Are you sure this should not be considered experimental? The API endpoints are brand new and could potentially change/be added to which may lead to updates in the OOP interface

Good point. Throw it under there as a new section

Would it be its own section, or just fall under this one?

Create a new entry under - Experimental: for this

BryanFauble · 2025-01-08T22:48:08Z

synapseclient/models/agent.py

+        agent_registration_id: The registration ID of the agent that will be used for this session.
+        etag: The etag of the agent session.
+    """
+


Check out the tables refactor PR for examples of the syntax for an Examples section. I'd like for the docstring to have scripts (Copy/pastable) that folks could run and get started.

synapseclient/models/agent.py

* Changes for async mixin * Remove arg * bug fix * generalizes send_job_and_wait_async * removes typing.Self --------- Co-authored-by: bwmac <[email protected]>

BWMac · 2025-01-15T15:49:56Z

synapseclient/client.py

-            return self._return_rest_body(response)
-        except Exception:
-            self.logger.exception("Error in rest_get_async")
+        response = await self._rest_call_async(


This error handling was preventing Synapse API errors from being surfaced to client users. All tests passed after making this change.

BWMac · 2025-01-15T15:50:23Z

synapseclient/models/services/storable_entity_components.py

@@ -4,10 +4,9 @@

 from synapseclient import Synapse
 from synapseclient.core.exceptions import SynapseError
-from synapseclient.models import Annotations

 if TYPE_CHECKING:


This was causing a circular import error

BWMac added 6 commits January 6, 2025 16:24

Adds async convenience functions

7f6022e

expose convenience functions

60dc255

updates convenience functions

3fd345c

updates agent_services

9c2c6d9

removes rest_get_async exception handling

52078b3

pre-commit fixes

fbcfcef

BWMac added 4 commits January 8, 2025 14:50

delete accidentally committed script

079a02c

adds initial agent implementation

5ae3257

clean up agent

84edb76

adds missing docstrings

88c6f06

BWMac changed the title ~~WIP [SYNPY-1544] Synapse Agent OOP Model~~ [SYNPY-1544] Synapse Agent OOP Model Jan 8, 2025

pre-commit

f34e9cc